Over the last decades a really tough competitive environment has been observed in shipbuilding sector. Under these circumstances shipyards desire to reduce product cycle time in order to manufacture the product as soon as possible. For this reason it is required to make some alterations in shipyard production system in order to reduce cycle time. In this study a panel fabrication line used in a shipyard, has been considered. The workstations of the panel line have been modeled by using ARENA simulation software and the effects of matrix module assembly on panel line throughput, have been determined.